Basic Qsys Tcl Script Fails (EModuleProperty)

You're confusing a couple different things.

a) qsys-script as you are running it is intended to modify .qsys systems, not modules (_hw.tcl)

b) the TCL reference (qsys_tcl.pdf) describes the TCL used in the _hw.tcl files, not the TCL used in qsys-script scripts.

c) the TCL commands in qsys-script scripts are described in qsys_intro.pdf (page 47)

d) the specific TCL example you're citing is for Instance scripts, which are another can of worms. Is that really what you're trying to do?

As a trivial qsys-script example, if you've got a .qsys with a PIO instance called pio_0, the following script will change it's width to 64 and save the results.

package require -exact qsys 13.1
set_instance_parameter_value pio_0 {width} {64}
save_system